Dataset Information

Vidjil: A Web Platform for Analysis of High-Throughput Repertoire Sequencing.

ABSTRACT:

Background

The B and T lymphocytes are white blood cells playing a key role in the adaptive immunity. A part of their DNA, called the V(D)J recombinations, is specific to each lymphocyte, and enables recognition of specific antigenes. Today, with new sequencing techniques, one can get billions of DNA sequences from these regions. With dedicated Repertoire Sequencing (RepSeq) methods, it is now possible to picture population of lymphocytes, and to monitor more accurately the immune response as well as pathologies such as leukemia.

Methods and results

Vidjil is an open-source platform for the interactive analysis of high-throughput sequencing data from lymphocyte recombinations. It contains an algorithm gathering reads into clonotypes according to their V(D)J junctions, a web application made of a sample, experiment and patient database and a visualization for the analysis of clonotypes along the time. Vidjil is implemented in C++, Python and Javascript and licensed under the GPLv3 open-source license. Source code, binaries and a public web server are available at http://www.vidjil.org and at http://bioinfo.lille.inria.fr/vidjil. Using the Vidjil web application consists of four steps: 1. uploading a raw sequence file (typically a FASTQ); 2. running RepSeq analysis software; 3. visualizing the results; 4. annotating the results and saving them for future use. For the end-user, the Vidjil web application needs no specific installation and just requires a connection and a modern web browser. Vidjil is used by labs in hematology or immunology for research and clinical applications.

SUBMITTER: Duez M

PROVIDER: S-EPMC5106020 | biostudies-literature | 2016

REPOSITORIES: biostudies-literature

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Publications

Vidjil: A Web Platform for Analysis of High-Throughput Repertoire Sequencing.

Duez Marc M Giraud Mathieu M Herbert Ryan R Rocher Tatiana T Salson Mikaël M Thonier Florian F

PloS one 20161111 11

<h4>Background</h4>The B and T lymphocytes are white blood cells playing a key role in the adaptive immunity. A part of their DNA, called the V(D)J recombinations, is specific to each lymphocyte, and enables recognition of specific antigenes. Today, with new sequencing techniques, one can get billions of DNA sequences from these regions. With dedicated Repertoire Sequencing (RepSeq) methods, it is now possible to picture population of lymphocytes, and to monitor more accurately the immune respon ...[more]

PMID: 27835690

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Dataset Information

Vidjil: A Web Platform for Analysis of High-Throughput Repertoire Sequencing.

Background

Methods and results

Publications

Vidjil: A Web Platform for Analysis of High-Throughput Repertoire Sequencing.

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